SMTL ID : 8p5f.1

Human wild-type GAPDH,orthorhombic form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 24 residues within 4Å: Chain A: N.9, G.10, F.11, G.12, R.13, I.14, N.34, D.35, P.36, F.37, I.38, E.79, R.80, S.98, T.99, G.100, F.102, S.122, A.123, C.152, A.183, N.316, Y.320 Chain D: P.191 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.14, A:I.14, A:Y.320 Hydrogen bonds: A:N.9, A:F.11, A:F.11, A:R.13, A:I.14, A:N.34, A:R.80, A:N.316 Water bridges: A:F.11, A:G.12, A:G.15, A:R.16, A:G.100, A:S.122, A:A.183, A:A.183 pi-Stacking: A:F.37 NAD.2: 25 residues within 4Å: Chain B: N.9, G.10, F.11, G.12, R.13, I.14, N.34, D.35, P.36, F.37, I.38, E.79, R.80, S.98, T.99, G.100, F.102, S.122, A.123, C.152, A.183, N.316, E.317, Y.320 Chain C: P.191 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:I.14, B:I.14, B:Y.320 Hydrogen bonds: B:N.9, B:F.11, B:F.11, B:R.13, B:I.14, B:N.34, B:R.80, B:N.316 Water bridges: B:F.11, B:G.12, B:G.15, B:R.16, B:G.100, B:S.122, B:A.183, B:A.183 pi-Stacking: B:F.37 NAD.3: 24 residues within 4Å: Chain B: P.191 Chain C: N.9, G.10, F.11, G.12, R.13, I.14, N.34, D.35, P.36, F.37, I.38, E.79, R.80, S.98, T.99, G.100, F.102, S.122, A.123, C.152, A.183, N.316, Y.320 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:I.14, C:I.14, C:Y.320 Hydrogen bonds: C:F.11, C:F.11, C:R.13, C:I.14, C:N.34, C:R.80, C:N.316 Water bridges: C:N.9, C:N.9, C:G.12, C:G.15, C:R.16, C:R.16, C:G.100, C:S.122, C:A.183, C:A.183, C:E.317, C:E.317 pi-Stacking: C:F.37 NAD.7: 23 residues within 4Å: Chain A: P.191 Chain D: N.9, G.10, F.11, G.12, R.13, I.14, N.34, D.35, P.36, F.37, I.38, R.80, S.98, T.99, G.100, F.102, S.122, A.123, C.152, A.183, N.316, Y.320 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:I.14, D:Y.320 Hydrogen bonds: D:F.11, D:R.13, D:I.14, D:N.34, D:R.80, D:N.316 Water bridges: D:N.9, D:R.16 pi-Stacking: D:F.37

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 3 residues within 4Å: Chain C: E.106, D.127 Ligands: ACT.5 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:E.106, C:E.106, C:D.127, ACT.5 ZN.6: 1 residues within 4Å: Chain C: E.335 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.335, H2O.20, H2O.22

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 5 residues within 4Å: Chain C: T.104, E.106, A.126, D.127 Ligands: ZN.4 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Medvedeva, M.V. et al., S-nitrosylation and S-glutathionylation of GAPDH: Similarities, differences, and relationships. Biochim Biophys Acta Gen Subj (2023)

Release Date

2023-07-05

Peptides

Glyceraldehyde-3-phosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
DDD

C
EEE

D
GGG

Glyceraldehyde-3-phosphate dehydrogenase

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